Usando o merge no R

> matchesfolhas <-read.delim(file="folha-rRNA.sam.ids", header=FALSE, stringsAsFactors=FALSE)
> colnames(matchesfolhas) <- c('IDread','IDsilva')
> silvaclass <- read.delim(file="../../../tmp/SILVA_119.txt", header=FALSE, stringsAsFactors=FALSE)
> colnames(silvaclass) <- c('IDsilva','IDclass')
> res <- merge(x=matchesfolhas, y=silvaclass, by='IDsilva')

Para procurar vetor de strings

subset(res,IDclass %in% outralistaqualquer)

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